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David Houle

Publications and source records attributed to David Houle.

17 recordsLinked to original sources
PubMed2007

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila.

Spontaneous mutations are the source of genetic variation required for evolutionary change, and are therefore important for many aspects of evolutionary biology. For example, the divergence between taxa at neutrally evolving sites in the genome is proportional to the per nucleotide mutation rate, u (ref. 1), and this can be used to date speciation events by assuming a molecular clock. The overall rate of occurrence of deleterious mutations in the genome each generation (U) appears in theories of nucleotide divergence and polymorphism, the evolution of sex and recombination, and the evolutionary consequences of inbreeding. However, estimates of U based on changes in allozymes or DNA sequences and fitness traits are discordant. Here we directly estimate u in Drosophila melanogaster by scanning 20 million bases of DNA from three sets of mutation accumulation lines by using denaturing high-performance liquid chromatography. From 37 mutation events that we detected, we obtained a mean estimate for u of 8.4 x 10(-9) per generation. Moreover, we detected significant heterogeneity in u among the three mutation-accumulation-line genotypes. By multiplying u by an estimate of the fraction of mutations that are deleterious in natural populations of Drosophila, we estimate that U is 1.2 per diploid genome. This high rate suggests that selection against deleterious mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction.

Animals↗
PubMed2005

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression.

Mutation is the ultimate source of biological diversity because it generates the variation that fuels evolution. Gene expression is the first step by which an organism translates genetic information into developmental change. Here we estimate the rate at which mutation produces new variation in gene expression by measuring transcript abundances across the genome during the onset of metamorphosis in 12 initially identical Drosophila melanogaster lines that independently accumulated mutations for 200 generations. We find statistically significant mutational variation for 39% of the genome and a wide range of variability across corresponding genes. As genes are upregulated in development their variability decreases, and as they are downregulated it increases, indicating that developmental context affects the evolution of gene expression. A strong correlation between mutational variance and environmental variance shows that there is the potential for widespread canalization. By comparing the evolutionary rates that we report here with differences between species, we conclude that gene expression does not evolve according to strictly neutral models. Although spontaneous mutations have the potential to generate abundant variation in gene expression, natural variation is relatively constrained.

Animals↗
PubMed2005

Sensory bias as an explanation for the evolution of mate preferences.

The sensory bias model of sexual selection posits that female mating preferences are by-products of natural selection on sensory systems. Although sensory bias was proposed 20 years ago, its critical assumptions remain untested. This paradox arises because sensory bias has been used to explain two different phenomena. First, it has been used as a hypothesis about signal design, that is, that males evolve traits that stimulate female sensory systems. Second, sensory bias has been used as a hypothesis for the evolution of female preference itself, that is, to explain why females exhibit particular preferences. We focus on this second facet. First, we clarify the unique features of sensory bias relative to the alternative models by considering each in the same quantitative genetic framework. The key assumptions of sensory bias are that natural selection is the predominant evolutionary mechanism that affects preference and that sexual selection on preferences is quantitatively negligible. We describe four studies that would test these assumptions and review what we can and cannot infer about sensory bias from existing studies. We suggest that the importance of sensory bias as an explanation for the evolution of female preferences remains to be determined.

Animals↗
PubMed2005

The dimensionality of genetic variation for wing shape in Drosophila melanogaster.

Absolute constraints are limitations on genetic variation that preclude evolutionary change in some aspect of the phenotype. Absolute constraints may reflect complete absence of variation, lack of genetic variation that extends the range of phenotypes beyond some limit, or lack of additive genetic variation. This last type of absolute constraint is bidirectional, because the mean cannot evolve to be larger or smaller. Most traits do possess genetic variation, so bidirectional absolute constraints are most likely to be detected in a multivariate context, where they would reflect combinations of traits, or dimensions in phenotype space that cannot evolve. A bidirectional absolute constraint will cause the additive genetic covariance matrix (G) to have a rank less than the number of traits studied. In this study, we estimate the rank of the G-matrix for 20 aspects of wing shape in Drosophila melanogaster. Our best estimates of matrix rank are 20 in both sexes. Lower 95% confidence intervals of rank are 17 for females and 18 for males. We therefore find little evidence of bidirectional absolute constraints. We discuss the importance of this result for resolving the relative roles of selection and drift processes versus constraints in the evolution of wing shape in Drosophila.

Animals↗
PubMed2004

Naturally segregating quantitative trait loci affecting wing shape of Drosophila melanogaster.

Variation in vein position and wing shape of Drosophila melanogaster depends on many genes. In the following, we report the results of a QTL analysis of wing shape in D. melanogaster. We identified QTL responsible for natural variation for wing shape and analyzed their interactions with developmental genetic signaling pathways important for vein positioning. The QTL analysis indicated that the total number of QTL segregating in this population is likely to be very large. The locations of putative QTL identified in this study were compared to those identified in previous studies and, while there is more correspondence across studies than expected by chance on the third chromosome, the studies appear to have identified different QTL. Using a complementation design, we tested for interactions among these QTL with the Hedgehog and Decapentaplegic signaling pathways, which are important for the development and position of vein pairs L3-L4 and L2-L5. Three QTL showed strong interactions with these two pathways, supporting the hypothesis that these QTL are involved in these pathways. Naturally segregating variation can therefore act through known signaling pathways to produce variation in vein position.

Animals↗
PubMed2004

Two classes of deleterious recessive alleles in a natural population of zebrafish, Danio rerio.

Natural populations carry deleterious recessive alleles which cause inbreeding depression. We compared mortality and growth of inbred and outbred zebrafish, Danio rerio, between 6 and 48 days of age. Grandparents of the studied fish were caught in the wild. Inbred fish were generated by brother-sister mating. Mortality was 9% in outbred fish, and 42% in inbred fish, which implies at least 3.6 lethal equivalents of deleterious recessive alleles per zygote. There was no significant inbreeding depression in the growth, perhaps because the surviving inbred fish lived under less crowded conditions. In contrast to alleles that cause embryonic and early larval mortality in the same population, alleles responsible for late larval and early juvenile mortality did not result in any gross morphological abnormalities. Thus, deleterious recessive alleles that segregate in a wild zebrafish population belong to two sharply distinct classes: early-acting, morphologically overt, unconditional lethals; and later-acting, morphologically cryptic, and presumably milder alleles.

Alleles↗
PubMed2004

Mutation accumulation and the effect of copia insertions in Drosophila melanogaster.

Repeated efforts to estimate the genomic deleterious mutation rate per generation (U) in Drosophila melanogaster have yielded inconsistent estimates ranging from 0.01 to nearly 1. We carried out a mutation-accumulation experiment with a cryopreserved control population in hopes of resolving some of the uncertainties raised by these estimates. Mutation accumulation (MA) was carried out by brother sister mating of 150 sublines derived from two inbred lines. Fitness was measured under conditions chosen to mimic the ancestral laboratory environment of these genotypes. We monitored the insertions of a transposable element, copia, that proved to accumulate at the unusually high rate of 0.24 per genome per generation in one of our MA lines. Mutational variance in fitness increased at a rate consistent with previous studies, yielding a mutational coefficient of variation greater than 3%. The performance of the cryopreserved control relative to the MA lines was inconsistent, so estimates of mutation rate by the Bateman-Mukai method are suspect. Taken at face value, these data suggest a modest decline in fitness of about 0.3% per generation. The element number of copia was a significant predictor of fitness within generations; on average, insertions caused a 0.76% loss in fitness, although the confidence limits on this estimate are wide.

Animals↗
PubMed2004

Comparing strengths of directional selection: how strong is strong?

The fundamental equation in evolutionary quantitative genetics, the Lande equation, describes the response to directional selection as a product of the additive genetic variance and the selection gradient of trait value on relative fitness. Comparisons of both genetic variances and selection gradients across traits or populations require standardization, as both are scale dependent. The Lande equation can be standardized in two ways. Standardizing by the variance of the selected trait yields the response in units of standard deviation as the product of the heritability and the variance-standardized selection gradient. This standardization conflates selection and variation because the phenotypic variance is a function of the genetic variance. Alternatively, one can standardize the Lande equation using the trait mean, yielding the proportional response to selection as the product of the squared coefficient of additive genetic variance and the mean-standardized selection gradient. Mean-standardized selection gradients are particularly useful for summarizing the strength of selection because the mean-standardized gradient for fitness itself is one, a convenient benchmark for strong selection. We review published estimates of directional selection in natural populations using mean-standardized selection gradients. Only 38 published studies provided all the necessary information for calculation of mean-standardized gradients. The median absolute value of multivariate mean-standardized gradients shows that selection is on average 54% as strong as selection on fitness. Correcting for the upward bias introduced by taking absolute values lowers the median to 31%, still very strong selection. Such large estimates clearly cannot be representative of selection on all traits. Some possible sources of overestimation of the strength of selection include confounding environmental and genotypic effects on fitness, the use of fitness components as proxies for fitness, and biases in publication or choice of traits to study.

Models, Genetic↗
PubMed2003

Automated measurement of Drosophila wings.

BACKGROUND: Many studies in evolutionary biology and genetics are limited by the rate at which phenotypic information can be acquired. The wings of Drosophila species are a favorable target for automated analysis because of the many interesting questions in evolution and development that can be addressed with them, and because of their simple structure. RESULTS: We have developed an automated image analysis system (WINGMACHINE) that measures the positions of all the veins and the edges of the wing blade of Drosophilid flies. A video image is obtained with the aid of a simple suction device that immobilizes the wing of a live fly. Low-level processing is used to find the major intersections of the veins. High-level processing then optimizes the fit of an a priori B-spline model of wing shape. WINGMACHINE allows the measurement of 1 wing per minute, including handling, imaging, analysis, and data editing. The repeatabilities of 12 vein intersections averaged 86% in a sample of flies of the same species and sex. Comparison of 2400 wings of 25 Drosophilid species shows that wing shape is quite conservative within the group, but that almost all taxa are diagnosably different from one another. Wing shape retains some phylogenetic structure, although some species have shapes very different from closely related species. The WINGMACHINE system facilitates artificial selection experiments on complex aspects of wing shape. We selected on an index which is a function of 14 separate measurements of each wing. After 14 generations, we achieved a 15 S.D. difference between up and down-selected treatments. CONCLUSION: WINGMACHINE enables rapid, highly repeatable measurements of wings in the family Drosophilidae. Our approach to image analysis may be applicable to a variety of biological objects that can be represented as a framework of connected lines.

Animals↗
PubMed2003

Comparing G matrices: are common principal components informative?

Common principal components (CPC) analysis is a technique for assessing whether variance-covariance matrices from different populations have similar structure. One potential application is to compare additive genetic variance-covariance matrices, G. In this article, the conditions under which G matrices are expected to have common PCs are derived for a two-locus, two-allele model and the model of constrained pleiotropy. The theory demonstrates that whether G matrices are expected to have common PCs is largely determined by whether pleiotropic effects have a modular organization. If two (or more) populations have modules and these modules have the same direction, the G matrices have a common PC, regardless of allele frequencies. In the absence of modules, common PCs exist only for very restricted combinations of allele frequencies. Together, these two results imply that, when populations are evolving, common PCs are expected only when the populations have modules in common. These results have two implications: (1) In general, G matrices will not have common PCs, and (2) when they do, these PCs indicate common modular organization. The interpretation of common PCs identified for estimates of G matrices is discussed in light of these results.

Data Interpretation, Statistical↗
PubMed2002

Consequences of hierarchical allocation for the evolution of life-history traits.

Resource allocation within individuals may often be hierarchical, and this may have important effects on genetic correlations and on trait evolution. For example, organisms may divide energy between reproduction and somatic growth and then subdivide reproductive resources. Genetic variation in allocation to pathways early in such hierarchies (e.g., reproduction) can cause positive genetic correlations between traits that trade off (e.g., offspring size and number) because some individuals invest more resources in reproduction than others. We used quantitative-genetic models to explore the evolutionary implications of allocation hierarchies. Our results showed that when variation in allocation early in the hierarchy exceeds subsequent variation in allocation, genetic covariances and initial responses to selection do not reflect trade-offs occurring at later levels in the hierarchy. This general pattern was evident for many starting allocations and optima and for whether traits contributed multiplicatively or additively to fitness. Finally, artificial selection on a single trait revealed masked trade-offs when variation in early allocation was comparable to subsequent variation in allocation. This result confirms artificial selection as a powerful, but not foolproof, method of detecting trade-offs. Thus, allocation hierarchies can profoundly affect life-history evolution by causing traits to evolve in the opposite direction to that predicted by trade-offs.

Animal Population Groups↗
PubMed2002

Natural selection in a bottle.

The study of natural selection in laboratory systems undergoing experimental evolution can provide important insights into the relationship between natural selection and adaptation. We studied selection on the norm of reaction of age at first reproduction in a laboratory population of Drosophila melanogaster. This population had been selected on a discrete generation schedule in the laboratory for more than 600 generations. Using genetically marked strains, we studied development time, size, female fecundity, and viability of flies that began development at different times relative to the initiation of each bottle. Only flies that began development within 30 h of the initiation of the bottle were reliably able to eclose before the next transfer. Theory predicts that flies initiating development around this critical time should decrease size at maturity to ensure eclosion by the 14-d deadline, but late flies are not smaller. This result suggests an unknown constraint on response to selection on age at maturity in this population. Ultimately, laboratory systems provide the best opportunity for the study of natural selection, genetic variation, and evolutionary response in the same population.

Aging↗
PubMed2002

A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish.

Despite the importance of selection against deleterious mutations in natural populations, reliable estimates of the genomic numbers of mutant alleles in wild populations are scarce. We found that, in wild-caught bluefin killifish Lucania goodei (Fundulidae) and wild-caught zebrafish Danio rerio (Cyprinidae), the average numbers of recessive lethal alleles per individual are 1.9 (95% confidence limits 1.3 to 2.6) and 1.4 (95% confidence limits 1.0 to 2.0), respectively. These results, together with data on several Drosophila species and on Xenopus laevis, show that phylogenetically distant animals with different genome sizes and numbers of genes carry similar numbers of lethal mutations.

Alleles↗
PubMed2002

Coevolution of costly mate choice and condition-dependent display of good genes.

Females often choose their mates, instead of mating at random, even when a father contributes nothing but genes to his offspring. Costly female preferences for males with exaggerated traits that reduce viability, such as the peacock's tail, are particularly puzzling. Such preferences can evolve if directly favoured by natural selection or when the exaggerated trait, although maladaptive per se, indicates high overall quality of the male's genotype. Two recent analyses suggested that the advantage to mate choice based on genetic quality is too weak to explain extreme cases of exaggeration of display traits and the corresponding preferences. We studied coevolution of a female mate-preference function and a genotype-dependent male display function where mutation supplies variation in genotype quality and mate preference is costly. Preference readily evolves, often causing extreme exaggeration of the display. Mate choice and trait expression can approach an equilibrium, or a limit cycle, or exaggeration can proceed forever, eventually causing extinction.

Animals↗
PubMed2002

Interpretation of the results of common principal components analyses.

Common principal components (CPC) analysis is a new tool for the comparison of phenotypic and genetic variance-covariance matrices. CPC was developed as a method of data summarization, but frequently biologists would like to use the method to detect analogous patterns of trait correlation in multiple populations or species. To investigate the properties of CPC, we simulated data that reflect a set of causal factors. The CPC method performs as expected from a statistical point of view, but often gives results that are contrary to biological intuition. In general, CPC tends to underestimate the degree of structure that matrices share. Differences of trait variances and covariances due to a difference in a single causal factor in two otherwise identically structured datasets often cause CPC to declare the two datasets unrelated. Conversely, CPC could identify datasets as having the same structure when causal factors are different. Reordering of vectors before analysis can aid in the detection of patterns. We urge caution in the biological interpretation of CPC analysis results.

Analysis of Variance↗
PubMed2000

Fluctuating Asymmetry as a Bioindicator of Stress: Comparing Efficacy of Analyses Involving Multiple Traits.

Researchers have suggested fluctuating asymmetry (FA) as an indicator of environmental stress and have usually tested this assertion by examining relations between FA of single traits and stress. Fluctuating asymmetry stress relations are real but are typically weak and difficult to detect. Researchers would like to maximize the probability of detecting FA-stress relations when they exist. We assert that analyses based on the FA of multiple traits may provide better methods for detecting stress. In this article, we used computer simulations to compare the ability of six analyses to detect differences in FA between stressed and unstressed populations. We show that the optimal analysis depends upon the underlying form of the FA distributions. We also show that two of the analyses had inflated Type I errors in some situations. Finally, we quantify the advantage of our preferred analysis over those of single-trait FA in detecting stress.

bioindicator↗